embeddings/README.md

# Text Embeddings

Be sure to select the proper text embedding files for the model and dataset versions:

## BioCLIP 2

### Files

```
txt_emb_bioclip-2.json
txt_emb_bioclip-2.npy
txt_emb_species.json and txt_emb_species.npy: duplicates of txt_emb_bioclip-2 files to support pybioclip backwards compatibility
```

### Generation

[BioCLIP 2 text embeddings of TreeOfLife-200M](txt_emb_bioclip-2.npy) were generated with [`make_txt_embedding.py`](https://github.com/Imageomics/TreeOfLife-toolbox/blob/main/processing/scripts/make_txt_embedding.py),  using the [`txt_emb_bioclip-2.json`](txt_emb_bioclip-2.json) to provide the 7-rank Linnean taxonomic names. These text embeddings match to the BioCLIP 2 training dataset, specified by the [catalog parquet from Revision a8f38b4](https://huggingface.co/datasets/imageomics/TreeOfLife-200M/blob/a8f38b4388579862c56ae57d6f094c2ac0e92e12/dataset/catalog.parquet). Note that [`txt_emb_species.npy`](txt_emb_species.npy) and [`txt_emb_species.json`](txt_emb_species.json) are duplicates of the BioCLIP 2 files, included here to maintain [pybioclip](http://github.com/Imageomics/pybioclip) functionality for versions 2.1.x and earlier.

## BioCLIP 2.5 Huge

### Files

```
txt_emb_bioclip-2.5-vith14.json
txt_emb_bioclip-2.5-vith14.npy
```

### Generation

The [BioCLIP 2.5 Huge text embeddings of TreeOfLife-200M](txt_emb_bioclip-2.5-vith14.npy) were also generated with [`make_txt_embedding.py`](https://github.com/Imageomics/TreeOfLife-toolbox/blob/main/processing/scripts/make_txt_embedding.py), but using the [`txt_emb_bioclip-2.5-vith14.json`](txt_emb_bioclip-2.5-vith14.json) to provide the 7-rank Linnean taxonomic names. These text embeddings match to the BioCLIP 2.5 Huge training dataset, specified by the catalog parquet added in [commit 97e2340](https://huggingface.co/datasets/imageomics/TreeOfLife-200M/commit/97e2340877d3a2ccad78078431fa68f404ed4870).

## Taxonomic JSON Construction

The `JSON` files were created from the [TreeOfLife-200M catalog](../catalog.parquet) (if reproducing the process, be sure to use the correct revision for the intended model) and [`VernacularName.tsv` component of the GBIF Backbone Taxonomy](https://doi.org/10.15468/39omei) using [`make_txt_embedding_json.py`](https://github.com/Imageomics/TreeOfLife-toolbox/blob/main/processing/scripts/make_txt_embedding_json.py) through the following process:
* **Null Value Filtering:** Remove records where `kingdom` or `species` are `null`.
* **Deduplication:** Rows are deduplicated based on the combination of `kingdom`, `phylum`, `class`, `order`, `family`, `genus`, and `species`. This ensures that each unique taxonomic combination appears exactly once.
    * **Common Name Handling:** Currently, the catalog metadata often contains multiple common names for a single unique taxonomic combination. During processing, **the first English common name encountered** for a given unique taxonomic combination is retained. If English is not available, the first option of any language is used. We plan future improvements to establish a definitive 1-to-1 mapping or a more comprehensive common name strategy.
* **Corrupted Label Removal:** Records where any rank looks like a CSV-parsing leak, specifically an ISO-8601 timestamp `(^\d{4}-\d{2}-\d{2}T\d{2}:\d{2})` or the literal strings `true` / `false`, are removed. This was only necessary for the BioCLIP 2.5 Huge JSON.

### Structure

The JSON file is a single top-level array. Each element within this array is itself an array of two elements:

* **Inner Array (Index 0):** A list of strings representing the full taxonomic path from `kingdom` to `species`.
* **String (Index 1):** The common name associated with that taxonomic combination.

#### Example

```json
[
  [
    [
      "Plantae",
      "Bryophyta",
      "Bryopsida",
      "Bryales",
      "Bryaceae",
      "Bryum",
      "gracile"
    ],
      ""
  ],
  [
    [
      "Animalia",
      "Chordata",
      "Aves",
      "Passeriformes",
      "Mitrospingidae",
      "Orthogonys",
      "chloricterus"
    ],
      "Olive-green tanager"
  ],
  [
    [
      "Animalia",
      "Arthropoda",
      "Insecta",
      "Lepidoptera",
      "Lycaenidae",
      "Orthomiella",
      "rantaizana"
    ],
    "Chinese Straight-wing Blue"
  ],
]
```